GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Cereibacter sphaeroides ATCC 17029

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_011842387.1 RSPH17029_RS17510 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_03040
         (254 letters)



>NCBI__GCF_000015985.1:WP_011842387.1
          Length = 266

 Score =  253 bits (647), Expect = 2e-72
 Identities = 127/246 (51%), Positives = 181/246 (73%), Gaps = 3/246 (1%)

Query: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63
           L ++++ K +G+ EVLKGVSL  A G+V+SIIG+SGSGKSTFLR IN++E P AG +   
Sbjct: 8   LRLREIRKSFGTFEVLKGVSLDVAQGEVVSIIGASGSGKSTFLRSINVMEMPQAGTMDFG 67

Query: 64  NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123
           +        + GA       QLQ++R+ + MVFQ +NLW HMT ++N++ AP+ +    +
Sbjct: 68  DFHFDF---RKGAASHPTKVQLQKLRAEIGMVFQSYNLWPHMTVLQNVIHAPMTLRRTPR 124

Query: 124 AEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183
           A+A E+AE  LA++G+  ++D+YP  +SGG+QQRVAIARALAM+P +MLFDE TSALDPE
Sbjct: 125 AQAVEEAEALLARIGLYEKRDSYPARLSGGQQQRVAIARALAMKPRLMLFDEVTSALDPE 184

Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243
           LV +VL +M +LA +G TM++VTHE+ FAR+VS++++F  +GV+ E G P  VL NP+S 
Sbjct: 185 LVHEVLVLMASLAADGMTMLLVTHEIAFARDVSSRVLFFDQGVMAEQGPPDRVLRNPESP 244

Query: 244 RLQQFL 249
           RL+QFL
Sbjct: 245 RLRQFL 250


Lambda     K      H
   0.317    0.131    0.364 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 188
Number of extensions: 4
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 254
Length of database: 266
Length adjustment: 24
Effective length of query: 230
Effective length of database: 242
Effective search space:    55660
Effective search space used:    55660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory